Importing Rigged Character and animations to Unreal Engine 4
I had the same issue. 

With me, the cause was that I had some objects selected (in Blender) that were not part of the animation. Exporting only "selected objects" (as per FBX export menu) that meant that my erroneously selected mesh was also selected - and was interpreted as a separate 'skeleton' in UE4. This 'skeleton' could obviously not be matched and gave the error ""Imported bone transform is different from original" on import. 

Correcting the selection of meshes before export in Blender solved the issue in this case.